The dried cubeb berries are widely used as medicinal herb and spicy condiment with special flavor. However, there is a significant definition discrepancy for cubeb berries. In this study, an efficient analytical method to characterize and discriminate two popular cubeb fruits (Litsea cubeba and Piper cubeba) was established. The aroma profiles of cubeb berries were evaluated by different extraction methods including hydro-distillation, simultaneous distillation/extraction, and solid-phase micro-extraction followed by gas chromatography-mass spectrometry-olfactometry (GC-MS-O). In total, 90 volatile compounds were identified by HD, SDE, and SPME combined with GC-MS. Principal component analysis was further applied and discriminated ambiguous cubeb berries by their unique aromas: Litsea cubeba was characterized by higher level of d-limonene (“fruit, citrus”), citral (“fruit, lemon”) and dodecanoic acid; α-cubebene (“herb”) was identified as a marker compound for Piper cubeba with higher camphor (“camphoraceous”), and linalool (“flower”). Flavor fingerprint combined with PCA could be applied as a promising method for identification of cubeb fruits and quality control for food and medicinal industries.